Research workbench
Structure of P22 tail-needle GP26 bound to xenon gas
Analyse Structure of P22 tail-needle GP26 bound to xenon gas in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3C9I
- Type
- protein
- Length
- 1,376 residues
- Chains
- 6
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Tail needle protein GP26
- UniProt
- P35837
- Ligands
- CA, XE, CL
- Pockets
- 10 · best druggability 0.52
Structure
x-ray diffraction · 5 distinct chains · 61% helix, 7% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, C | Tail needle protein GP26 | protein | 233 | 61% helix, 8% strand | P35837 |
| B | Tail needle protein GP26 | protein | 242 | 60% helix, 8% strand | P35837 |
| D | Tail needle protein GP26 | protein | 221 | 60% helix, 6% strand | P35837 |
| E | Tail needle protein GP26 | protein | 226 | 59% helix, 8% strand | P35837 |
| F | Tail needle protein GP26 | protein | 221 | 64% helix, 8% strand | P35837 |
Ligands and binding sites
- CA · Calcium ion · metal · 2 copies · chains A, B, C, D, E, F
- XE · Xenon · ion · 14 copies · chains A, B, C, D, E, F
- CL · Chloride ion · ion · 2 copies · chains A, B, C, D, E, F
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
10 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 277 | 0.52 | 0.75 | 41 | empty |
| 2 | 247 | 0.49 | 0.74 | 34 | empty |
| 3 | 205 | 0.49 | 0.76 | 29 | empty |
| 4 | 139 | 0.46 | 0.77 | 33 | empty |
| 5 | 93 | 0.39 | 0.77 | 22 | empty |
Interfaces
12 interfaces between chains.
- A–B · 5284 Ų buried · 103 hydrogen bonds · protein-protein
- B–C · 5091 Ų buried · 93 hydrogen bonds · protein-protein
- A–C · 5049 Ų buried · 93 hydrogen bonds · protein-protein
- D–F · 4811 Ų buried · 100 hydrogen bonds · protein-protein
- D–E · 4777 Ų buried · 91 hydrogen bonds · protein-protein
Compared structures
- 3C9I · Structure of P22 Tail-Needle GP26 Bound to Xenon Gas · the same entry in another collection · chain A against A, TM-score 1.00
Analyse
- Open in the research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides and crosslinks on the 3D structure
- Every structure of UniProt P35837
- Elsewhere: RCSB PDB 3C9I · PDBe 3C9I · UniProt P35837
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